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Detailed information for vg0335310167:

Variant ID: vg0335310167 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35310167
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.05, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

CTTACTTCCCTAAATGTTTGACGCTGTTGACTTTTTAAAGTATGTTTAACCATTTGTCTTATTCAAAAACTTTTGTGAAATATGTAAAACTATATGTATA[T/C]
ATAAAAGTATATTTAACAATAAATCAAATGATAGGAAAAGAATTAATTATTATTTAAATTTTTTTAAATAAGACGAACAGTCAAATATTTTTAAAAAAGT

Reverse complement sequence

ACTTTTTTAAAAATATTTGACTGTTCGTCTTATTTAAAAAAATTTAAATAATAATTAATTCTTTTCCTATCATTTGATTTATTGTTAAATATACTTTTAT[A/G]
TATACATATAGTTTTACATATTTCACAAAAGTTTTTGAATAAGACAAATGGTTAAACATACTTTAAAAAGTCAACAGCGTCAAACATTTAGGGAAGTAAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.30%	41.60%	0.17%	0.00%	NA
All Indica	2759	39.40%	60.30%	0.25%	0.00%	NA
All Japonica	1512	97.40%	2.50%	0.07%	0.00%	NA
Aus	269	19.30%	80.70%	0.00%	0.00%	NA
Indica I	595	69.40%	30.30%	0.34%	0.00%	NA
Indica II	465	23.20%	76.80%	0.00%	0.00%	NA
Indica III	913	34.40%	65.40%	0.22%	0.00%	NA
Indica Intermediate	786	32.10%	67.60%	0.38%	0.00%	NA
Temperate Japonica	767	98.00%	1.80%	0.13%	0.00%	NA
Tropical Japonica	504	95.40%	4.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	53.30%	46.70%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0335310167	T -> C	LOC_Os03g62330.1	3_prime_UTR_variant ; 142.0bp to feature; MODIFIER	silent_mutation	Average:66.286; most accessible tissue: Minghui63 root, score: 88.244	N	N	N	N
vg0335310167	T -> C	LOC_Os03g62314.1	upstream_gene_variant ; 781.0bp to feature; MODIFIER	silent_mutation	Average:66.286; most accessible tissue: Minghui63 root, score: 88.244	N	N	N	N
vg0335310167	T -> C	LOC_Os03g62340.1	downstream_gene_variant ; 2284.0bp to feature; MODIFIER	silent_mutation	Average:66.286; most accessible tissue: Minghui63 root, score: 88.244	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335310167	NA	9.12E-06	mr1910_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251